Variant report

Variant	rs3130258
Chromosome Location	chr6:33257162-33257163
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:370)
CpG islands
(count:244)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:370 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF1	chr6:33256924-33257584	K562	blood:	n/a	n/a
2	MAFK	chr6:33256893-33257518	K562	blood:	n/a	n/a
3	ZBTB33	chr6:33257084-33257511	A549	lung:	n/a	n/a
4	POLR2A	chr6:33257154-33257648	GM12892	blood:	n/a	n/a
5	POLR2A	chr6:33257145-33257642	K562	blood:	n/a	n/a
6	MAX	chr6:33256426-33257846	MCF-7	breast:	n/a	chr6:33257146-33257155
7	NFIC	chr6:33256604-33257762	GM12878	blood:	n/a	n/a
8	BHLHE40	chr6:33256750-33257983	K562	blood:	n/a	n/a
9	GTF2F1	chr6:33256900-33257650	Hela-S3	cervix:	n/a	n/a
10	GATA2	chr6:33256915-33257315	SH-SY5Y	brain:	n/a	n/a
11	NR2F2	chr6:33256806-33257622	K562	blood:	n/a	n/a
12	HCFC1	chr6:33256430-33258129	Hela-S3	cervix:	n/a	n/a
13	STAT3	chr6:33257052-33257492	MCF10A-Er-Src	breast:	n/a	chr6:33257209-33257220 chr6:33257305-33257316
14	TAF1	chr6:33256618-33257701	ECC-1	luminal epithelium:	n/a	n/a
15	TEAD4	chr6:33256798-33257957	K562	blood:	n/a	n/a
16	POLR2A	chr6:33256717-33257749	H1-neurons	neurons:	n/a	n/a
17	GABPA	chr6:33256535-33257900	A549	lung:	n/a	chr6:33256822-33256831
18	ZMIZ1	chr6:33256406-33257794	K562	blood:	n/a	n/a
19	MAFK	chr6:33256908-33257470	HepG2	liver:	n/a	n/a
20	HDAC2	chr6:33256725-33257525	K562	blood:	n/a	chr6:33257164-33257178
21	ATF2	chr6:33256650-33257659	GM12878	blood:	n/a	n/a
22	CUX1	chr6:33256742-33257691	K562	blood:	n/a	n/a
23	ELF1	chr6:33256607-33257500	K562	blood:	n/a	chr6:33257330-33257339 chr6:33257364-33257377
24	NFYB	chr6:33256613-33257359	K562	blood:	n/a	chr6:33257034-33257048 chr6:33257036-33257046 chr6:33257031-33257046
25	NFYB	chr6:33256824-33257417	Hela-S3	cervix:	n/a	chr6:33257034-33257048 chr6:33257036-33257046 chr6:33257031-33257046
26	POLR2A	chr6:33256672-33259552	PANC-1	pancreas:	n/a	n/a
27	FOS	chr6:33257132-33257437	MCF10A-Er-Src	breast:	n/a	chr6:33257217-33257229
28	TAF1	chr6:33256887-33257587	GM12878	blood:	n/a	n/a
29	MAFF	chr6:33257006-33257410	HepG2	liver:	n/a	n/a
30	MAX	chr6:33256326-33257887	HCT-116	colon:	n/a	chr6:33257146-33257155
31	SREBP1	chr6:33256021-33257935	GM12878	blood:	n/a	n/a
32	POLR2A	chr6:33256695-33257612	HepG2	liver:	n/a	n/a
33	POLR2A	chr6:33257101-33258647	HL-60	blood:	n/a	n/a
34	GABPA	chr6:33256682-33257642	HepG2	liver:	n/a	chr6:33256822-33256831
35	ELF1	chr6:33256680-33257730	MCF-7	breast:	n/a	chr6:33257330-33257339 chr6:33257364-33257377
36	MAX	chr6:33256497-33257665	MCF-7	breast:	n/a	chr6:33257146-33257155
37	SIX5	chr6:33256751-33257567	GM12878	blood:	n/a	chr6:33257302-33257311 chr6:33257300-33257309 chr6:33256847-33256861 chr6:33257298-33257312
38	ZNF143	chr6:33256775-33257731	GM12878	blood:	n/a	chr6:33257300-33257318 chr6:33257300-33257309 chr6:33257347-33257362 chr6:33257302-33257311
39	BHLHE40	chr6:33256768-33257813	GM12878	blood:	n/a	n/a
40	YY1	chr6:33256911-33257448	HCT-116	colon:	n/a	chr6:33257076-33257084 chr6:33257071-33257090 chr6:33257073-33257095
41	PML	chr6:33256693-33257970	K562	blood:	n/a	n/a
42	CEBPB	chr6:33256920-33257942	K562	blood:	n/a	n/a
43	FOS	chr6:33257150-33257388	MCF10A-Er-Src	breast:	n/a	chr6:33257217-33257229
44	GABPA	chr6:33256594-33257829	K562	blood:	n/a	chr6:33256822-33256831
45	BRCA1	chr6:33256764-33257602	Hela-S3	cervix:	n/a	n/a
46	JUND	chr6:33256796-33257777	K562	blood:	n/a	chr6:33256823-33256832 chr6:33257217-33257229
47	NR2C2	chr6:33256818-33257780	GM12878	blood:	n/a	n/a
48	REST	chr6:33256682-33257607	A549	lung:	n/a	n/a
49	TAF1	chr6:33257137-33257579	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr6:33256748-33260558	PANC-1	pancreas:	n/a	n/a

(count:244 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:33257112-33257162	SKMC	muscle:	n/a
2	chr6:33257112-33257162	HMEC	breast:	n/a
3	chr6:33257135-33257185	HCM	heart:	n/a
4	chr6:33257135-33257185	GM19239	blood:	n/a
5	chr6:33257135-33257185	NHDF-neo	bronchial:	n/a
6	chr6:33257137-33257187	PFSK-1	brain:	n/a
7	chr6:33257112-33257162	HEK293	kidney:	embryo
8	chr6:33257135-33257185	IMR90	lung:	fetal
9	chr6:33257135-33257185	HEK293	kidney:	embryo
10	chr6:33257112-33257162	H1-hESC	embryonic stem cell:	embryo
11	chr6:33257141-33257191	HCM	heart:	n/a
12	chr6:33257141-33257191	PFSK-1	brain:	n/a
13	chr6:33257135-33257185	AG09309	skin:	n/a
14	chr6:33257112-33257162	NH-A	brain:	n/a
15	chr6:33257137-33257187	NHDF-neo	bronchial:	n/a
16	chr6:33257135-33257185	GM12891	blood:	n/a
17	chr6:33257137-33257187	MCF-7	breast:	n/a
18	chr6:33257135-33257185	HCF	heart:	n/a
19	chr6:33257112-33257162	HRE	kidney:	n/a
20	chr6:33257135-33257185	HCT-116	colon:	n/a
21	chr6:33257137-33257187	NT2-D1	testis:	n/a
22	chr6:33257141-33257191	SAEC	small airway:	n/a
23	chr6:33257141-33257191	AG10803	skin:	n/a
24	chr6:33257112-33257162	AG04450	lung:	fetal
25	chr6:33257135-33257185	T-47D	breast:	n/a
26	chr6:33257137-33257187	HNPCEpiC	eye:	n/a
27	chr6:33257112-33257162	HCM	heart:	n/a
28	chr6:33257141-33257191	HUVEC	blood vessel:	n/a
29	chr6:33257112-33257162	AG09309	skin:	n/a
30	chr6:33257141-33257191	K562	blood:	n/a
31	chr6:33257141-33257191	LNCaP	prostate:	n/a
32	chr6:33257112-33257162	Hepatocyte	liver:	n/a
33	chr6:33257137-33257187	AoSMC	blood vessel:	n/a
34	chr6:33257141-33257191	AG09309	skin:	n/a
35	chr6:33257135-33257185	MCF-7	breast:	n/a
36	chr6:33257112-33257162	HIPEpiC	eye:	n/a
37	chr6:33257141-33257191	Caco-2	colon:	n/a
38	chr6:33257137-33257187	PrEC	prostate:	n/a
39	chr6:33257135-33257185	HCPEpiC	choroid plexus:	n/a
40	chr6:33257112-33257162	PANC-1	pancreas:	n/a
41	chr6:33257137-33257187	HRCEpiC	kidney:	n/a
42	chr6:33257141-33257191	Jurkat	blood:	n/a
43	chr6:33257112-33257162	HAEpiC	amniotic membrane:	n/a
44	chr6:33257141-33257191	SKMC	muscle:	n/a
45	chr6:33257135-33257185	H1-hESC	embryonic stem cell:	embryo
46	chr6:33257112-33257162	SK-N-SH	brain:	n/a
47	chr6:33257112-33257162	HNPCEpiC	eye:	n/a
48	chr6:33257141-33257191	HEEpiC	esophagus:	n/a
49	chr6:33257137-33257187	BJ	skin:	n/a
50	chr6:33257135-33257185	HepG2	liver:	n/a

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:33215515..33217773-chr6:33257117..33258844,2	K562	blood:
2	chr6:32937120..32939036-chr6:33257083..33259939,2	MCF-7	breast:
3	chr6:33256522..33259302-chr6:33375799..33380992,5	MCF-7	breast:
4	chr12:120728485..120731088-chr6:33255818..33258567,3	MCF-7	breast:
5	chr6:33256540..33259907-chr6:33358017..33361464,3	MCF-7	breast:
6	chr6:33255047..33257514-chr6:33384371..33386134,2	K562	blood:
7	chr6:32934202..32936578-chr6:33256185..33258696,2	K562	blood:
8	chr6:33170950..33173180-chr6:33254762..33258714,3	K562	blood:
9	chr6:33257047..33258013-chr6:33266596..33267410,2	MCF-7	breast:
10	chr6:33254516..33257651-chr6:33384634..33387572,3	K562	blood:
11	chr6:33256218..33259091-chr6:33279064..33284854,6	MCF-7	breast:
12	chr6:33255490..33258967-chr6:33375507..33378634,5	MCF-7	breast:
13	chr6:33254680..33257397-chr6:33405638..33407793,2	K562	blood:
14	chr6:33255667..33257365-chr6:33384673..33386459,3	MCF-7	breast:
15	chr6:33256889..33260224-chr6:33374160..33378303,4	K562	blood:
16	chr6:33247918..33248886-chr6:33256671..33257416,2	K562	blood:
17	chr12:48213261..48213880-chr6:33256853..33257420,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
PFDN6	TF binding region
WDR46	TF binding region
PFDN6	CpG island
WDR46	CpG island
ENSG00000264085	Chromatin interaction
ENSG00000227057	Chromatin interaction
ENSG00000112511	Chromatin interaction
ENSG00000237441	Chromatin interaction
ENSG00000197283	Chromatin interaction
ENSG00000223837	Chromatin interaction
ENSG00000232940	Chromatin interaction
ENSG00000061273	Chromatin interaction
ENSG00000204256	Chromatin interaction
ENSG00000231925	Chromatin interaction
ENSG00000200795	Chromatin interaction
ENSG00000204228	Chromatin interaction
ENSG00000112514	Chromatin interaction
ENSG00000237649	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000204257	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1755038	1.00[ASN][1000 genomes]
rs1755040	1.00[ASN][1000 genomes]
rs210190	1.00[ASN][1000 genomes]
rs213198	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2941555	1.00[ASN][1000 genomes]
rs3106196	1.00[ASN][1000 genomes]
rs3116713	1.00[ASN][1000 genomes]
rs3119026	1.00[ASN][1000 genomes]
rs3130013	1.00[ASN][1000 genomes]
rs3130021	0.84[EUR][1000 genomes]
rs3130023	1.00[ASN][1000 genomes]
rs3130026	1.00[ASN][1000 genomes]
rs3130104	1.00[ASN][1000 genomes]
rs3130257	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130273	1.00[ASN][1000 genomes]
rs35700288	1.00[ASN][1000 genomes]
rs36003672	1.00[ASN][1000 genomes]
rs449978	1.00[ASN][1000 genomes]
rs6910721	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830634	chr6:33161217-33330745	Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
2	nsv830635	chr6:33238005-33413787	Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	129 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33255800-33257800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
2	chr6:33255800-33258800	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr6:33256000-33258000	Active TSS	Psoas Muscle	Psoas
4	chr6:33256000-33258200	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr6:33256000-33258400	Active TSS	H1 Cell Line	embryonic stem cell
6	chr6:33256000-33258400	Active TSS	H9 Cell Line	embryonic stem cell
7	chr6:33256000-33258600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr6:33256000-33258600	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr6:33256200-33257800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr6:33256200-33258000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:33256200-33258000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
12	chr6:33256200-33258000	Active TSS	A549	lung
13	chr6:33256200-33258000	Active TSS	NHDF-Ad	bronchial
14	chr6:33256200-33258200	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr6:33256200-33258200	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr6:33256200-33258200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr6:33256200-33258400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr6:33256400-33257600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:33256400-33257600	Active TSS	Brain Inferior Temporal Lobe	brain
20	chr6:33256400-33257600	Active TSS	Fetal Heart	heart
21	chr6:33256400-33257600	Active TSS	Placenta Amnion	Placenta Amnion
22	chr6:33256400-33257600	Active TSS	Stomach Mucosa	stomach
23	chr6:33256400-33257800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:33256400-33257800	Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr6:33256400-33257800	Active TSS	Muscle Satellite Cultured Cells	--
26	chr6:33256400-33257800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr6:33256400-33257800	Active TSS	Esophagus	oesophagus
28	chr6:33256400-33257800	Active TSS	Fetal Intestine Small	intestine
29	chr6:33256400-33257800	Active TSS	Fetal Lung	lung
30	chr6:33256400-33257800	Active TSS	Lung	lung
31	chr6:33256400-33257800	Active TSS	Pancreas	Pancrea
32	chr6:33256400-33257800	Active TSS	Right Ventricle	heart
33	chr6:33256400-33257800	Active TSS	Sigmoid Colon	Sigmoid Colon
34	chr6:33256400-33257800	Active TSS	Small Intestine	intestine
35	chr6:33256400-33257800	Active TSS	HSMM	muscle
36	chr6:33256400-33257800	Active TSS	HUVEC	blood vessel
37	chr6:33256400-33257800	Active TSS	NHEK	skin
38	chr6:33256400-33257800	Active TSS	NHLF	lung
39	chr6:33256400-33257800	Active TSS	Osteobl	bone
40	chr6:33256400-33258000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
41	chr6:33256400-33258000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr6:33256400-33258000	Active TSS	HUES6 Cell Line	embryonic stem cell
43	chr6:33256400-33258000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr6:33256400-33258000	Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr6:33256400-33258000	Active TSS	Aorta	Aorta
46	chr6:33256400-33258000	Active TSS	Fetal Kidney	kidney
47	chr6:33256400-33258000	Active TSS	Left Ventricle	heart
48	chr6:33256400-33258000	Active TSS	GM12878-XiMat	blood
49	chr6:33256400-33258000	Active TSS	Hela-S3	cervix
50	chr6:33256400-33258000	Bivalent/Poised TSS	HepG2	liver

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